Just so I have a better picture of the situation, I perceive that you are the homeowner and this was obviously a remodel. When they installed the zone system did they reuse existing ducts or install new? What is the brand and model # of the zone system?
Off the bat I see one problem but need a little more info. What was the sensible and latent heat gain numbers?
You say that they want to install an additional 2 ton unit - how would this be connected to the zone system? With an additional furnace/air handler?